Imputation Report For Cohort: WTCCC

Per chromosome imputation report for cohort WTCCC.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 25.6.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 17693496 79.371
0.1 1220691 5.476
0.2 811049 3.638
0.3 617468 2.770
0.4 495367 2.222
0.5 405424 1.819
0.6 348644 1.564
0.7 290764 1.304
0.8 241135 1.082
0.9 167965 0.753
Total 22292003 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 1333464 5.982
0.4 1594714 7.154
0.5 2087218 9.363
0.6 2712129 12.166
0.7 3226998 14.476
0.8 3486713 15.641
0.9 7803643 35.006
1.0 47124 0.211
Total 22292003 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1345942 79.7599
0.1 89397 5.2976
0.2 57934 3.4331
0.3 45304 2.6847
0.4 37430 2.2181
0.5 30395 1.8012
0.6 27133 1.6079
0.7 21666 1.2839
0.8 18623 1.1036
0.9 13668 0.8100
Total 1687492

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 102306 6.0626
0.4 123216 7.3017
0.5 159741 9.4662
0.6 207463 12.2942
0.7 248457 14.7234
0.8 265194 15.7153
0.9 577626 34.2299
1.0 3489 0.2068
Total 1687492

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1506704 80.1031
0.1 100488 5.3424
0.2 66180 3.5184
0.3 49415 2.6271
0.4 38604 2.0524
0.5 32741 1.7407
0.6 28717 1.5267
0.7 23366 1.2422
0.8 20128 1.0701
0.9 14612 0.7768
Total 1880955

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 104290 5.5445
0.4 125973 6.6973
0.5 167537 8.9070
0.6 225763 12.0026
0.7 277451 14.7505
0.8 298195 15.8534
0.9 678170 36.0546
1.0 3576 0.1901
Total 1880955

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1270224 79.7069
0.1 87647 5.4999
0.2 55292 3.4696
0.3 43158 2.7082
0.4 34889 2.1893
0.5 29248 1.8353
0.6 24676 1.5484
0.7 20503 1.2866
0.8 16581 1.0405
0.9 11400 0.7154
Total 1593618

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 87243 5.4745
0.4 103639 6.5034
0.5 140596 8.8224
0.6 189808 11.9105
0.7 233026 14.6225
0.8 254232 15.9531
0.9 581652 36.4988
1.0 3422 0.2147
Total 1593618

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1227049 78.8301
0.1 82075 5.2728
0.2 60584 3.8921
0.3 44897 2.8843
0.4 34125 2.1923
0.5 27812 1.7867
0.6 24485 1.5730
0.7 21599 1.3876
0.8 19853 1.2754
0.9 14095 0.9055
Total 1556574

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 86606 5.5639
0.4 103230 6.6319
0.5 138191 8.8779
0.6 183713 11.8024
0.7 223539 14.3610
0.8 246091 15.8098
0.9 572213 36.7611
1.0 2991 0.1922
Total 1556574

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1151415 79.7524
0.1 76873 5.3246
0.2 53070 3.6759
0.3 40305 2.7917
0.4 31692 2.1951
0.5 24633 1.7062
0.6 22387 1.5506
0.7 18246 1.2638
0.8 14978 1.0374
0.9 10138 0.7022
Total 1443737

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 79499 5.5065
0.4 93612 6.4840
0.5 124811 8.6450
0.6 167946 11.6327
0.7 208542 14.4446
0.8 230392 15.9580
0.9 535342 37.0803
1.0 3593 0.2489
Total 1443737

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1103480 78.7379
0.1 81694 5.8292
0.2 52876 3.7729
0.3 40125 2.8631
0.4 32829 2.3425
0.5 25766 1.8385
0.6 22641 1.6155
0.7 17131 1.2224
0.8 15158 1.0816
0.9 9759 0.6963
Total 1401459

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 70614 5.0386
0.4 83074 5.9277
0.5 113610 8.1066
0.6 155185 11.0731
0.7 195753 13.9678
0.8 220607 15.7412
0.9 559043 39.8901
1.0 3573 0.2549
Total 1401459

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 993650 79.1716
0.1 69631 5.5480
0.2 47598 3.7925
0.3 35554 2.8329
0.4 28546 2.2745
0.5 23636 1.8833
0.6 18863 1.5030
0.7 16324 1.3007
0.8 12185 0.9709
0.9 9071 0.7228
Total 1255058

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 74813 5.9609
0.4 88562 7.0564
0.5 116656 9.2949
0.6 151989 12.1101
0.7 182312 14.5262
0.8 197684 15.7510
0.9 440874 35.1278
1.0 2168 0.1727
Total 1255058

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 982076 79.9015
0.1 64043 5.2105
0.2 44346 3.6080
0.3 32585 2.6511
0.4 27647 2.2494
0.5 21353 1.7373
0.6 19384 1.5771
0.7 15567 1.2665
0.8 13088 1.0648
0.9 9020 0.7339
Total 1229109

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 70169 5.7089
0.4 82312 6.6969
0.5 106170 8.6380
0.6 143133 11.6453
0.7 179179 14.5780
0.8 193940 15.7789
0.9 451553 36.7382
1.0 2653 0.2158
Total 1229109

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 746006 79.5217
0.1 53687 5.7229
0.2 34085 3.6333
0.3 24747 2.6379
0.4 20425 2.1772
0.5 15681 1.6715
0.6 14752 1.5725
0.7 11647 1.2415
0.8 9687 1.0326
0.9 7399 0.7887
Total 938116

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 51213 5.4591
0.4 61149 6.5183
0.5 82777 8.8237
0.6 112421 11.9837
0.7 137782 14.6871
0.8 152444 16.2500
0.9 338407 36.0730
1.0 1923 0.2050
Total 938116

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 869360 79.2817
0.1 60961 5.5594
0.2 39600 3.6113
0.3 28733 2.6203
0.4 24606 2.2440
0.5 20999 1.9150
0.6 16831 1.5349
0.7 14278 1.3021
0.8 12580 1.1472
0.9 8598 0.7841
Total 1096546

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 57844 5.2751
0.4 68408 6.2385
0.5 92033 8.3930
0.6 124598 11.3628
0.7 155836 14.2115
0.8 174303 15.8956
0.9 420520 38.3495
1.0 3004 0.2740
Total 1096546

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 856508 79.1912
0.1 59161 5.4699
0.2 36185 3.3456
0.3 30727 2.8410
0.4 24374 2.2536
0.5 20734 1.9170
0.6 17922 1.6570
0.7 14347 1.3265
0.8 12196 1.1276
0.9 9415 0.8705
Total 1081569

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 59451 5.4967
0.4 71362 6.5980
0.5 96060 8.8815
0.6 128347 11.8667
0.7 155761 14.4014
0.8 168231 15.5543
0.9 398560 36.8502
1.0 3797 0.3511
Total 1081569

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 829923 79.4763
0.1 56898 5.4488
0.2 35490 3.3986
0.3 30838 2.9532
0.4 22709 2.1747
0.5 18863 1.8064
0.6 16296 1.5606
0.7 12508 1.1978
0.8 12455 1.1927
0.9 8259 0.7909
Total 1044239

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 58803 5.6312
0.4 70280 6.7303
0.5 91267 8.7400
0.6 122922 11.7714
0.7 149002 14.2690
0.8 164334 15.7372
0.9 384979 36.8669
1.0 2652 0.2540
Total 1044239

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 617410 78.5403
0.1 42914 5.4591
0.2 27983 3.5597
0.3 22836 2.9050
0.4 17593 2.2380
0.5 15491 1.9706
0.6 12571 1.5991
0.7 11390 1.4489
0.8 9713 1.2356
0.9 8205 1.0438
Total 786106

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 40509 5.1531
0.4 48913 6.2222
0.5 67236 8.5530
0.6 92301 11.7415
0.7 115339 14.6722
0.8 127546 16.2250
0.9 292089 37.1564
1.0 2173 0.2764
Total 786106

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 549321 79.2703
0.1 38932 5.6181
0.2 26290 3.7938
0.3 18087 2.6101
0.4 15524 2.2402
0.5 11868 1.7126
0.6 10101 1.4576
0.7 9077 1.3099
0.8 7752 1.1187
0.9 6020 0.8687
Total 692972

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 40345 5.8220
0.4 49231 7.1043
0.5 64482 9.3051
0.6 84661 12.2171
0.7 100061 14.4394
0.8 107419 15.5012
0.9 245405 35.4134
1.0 1368 0.1974
Total 692972

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 492518 79.4604
0.1 33386 5.3863
0.2 22342 3.6045
0.3 16725 2.6983
0.4 14286 2.3048
0.5 11783 1.9010
0.6 8922 1.4394
0.7 7909 1.2760
0.8 6586 1.0626
0.9 5371 0.8665
Total 619828

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 38644 6.2346
0.4 47577 7.6758
0.5 61860 9.9802
0.6 78193 12.6153
0.7 91166 14.7083
0.8 96437 15.5587
0.9 204698 33.0250
1.0 1253 0.2022
Total 619828

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 526006 79.3973
0.1 37760 5.6996
0.2 22868 3.4518
0.3 19158 2.8918
0.4 13968 2.1084
0.5 12143 1.8329
0.6 10691 1.6137
0.7 9507 1.4350
0.8 6350 0.9585
0.9 4048 0.6110
Total 662499

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 45638 6.8888
0.4 54667 8.2516
0.5 69965 10.5608
0.6 86308 13.0276
0.7 98309 14.8391
0.8 105731 15.9594
0.9 201179 30.3667
1.0 702 0.1060
Total 662499

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 447828 79.1034
0.1 30175 5.3300
0.2 23007 4.0639
0.3 15474 2.7333
0.4 13553 2.3940
0.5 11126 1.9653
0.6 8804 1.5551
0.7 7903 1.3960
0.8 5663 1.0003
0.9 2597 0.4587
Total 566130

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 49426 8.7305
0.4 58937 10.4105
0.5 72219 12.7566
0.6 80783 14.2693
0.7 82831 14.6311
0.8 83333 14.7198
0.9 138073 24.3889
1.0 528 0.0933
Total 566130

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 484441 78.9282
0.1 33988 5.5375
0.2 23447 3.8201
0.3 17670 2.8789
0.4 13935 2.2704
0.5 11035 1.7979
0.6 9453 1.5401
0.7 8068 1.3145
0.8 6555 1.0680
0.9 5182 0.8443
Total 613774

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 35898 5.8487
0.4 44056 7.1779
0.5 60214 9.8105
0.6 77949 12.7000
0.7 90889 14.8082
0.8 96319 15.6929
0.9 207261 33.7683
1.0 1188 0.1936
Total 613774

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 328366 77.4331
0.1 28336 6.6820
0.2 18721 4.4147
0.3 12930 3.0491
0.4 9591 2.2617
0.5 8155 1.9231
0.6 6711 1.5825
0.7 5748 1.3555
0.8 3915 0.9232
0.9 1591 0.3752
Total 424064

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 47353 11.1665
0.4 54546 12.8627
0.5 60140 14.1818
0.6 60491 14.2646
0.7 56548 13.3348
0.8 57040 13.4508
0.9 87544 20.6441
1.0 402 0.0948
Total 424064

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 386835 79.4252
0.1 27298 5.6048
0.2 18103 3.7169
0.3 13424 2.7562
0.4 11186 2.2967
0.5 8898 1.8269
0.6 7669 1.5746
0.7 5944 1.2204
0.8 4671 0.9591
0.9 3015 0.6190
Total 487043

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 31294 6.4253
0.4 38617 7.9289
0.5 51012 10.4738
0.6 64486 13.2403
0.7 70903 14.5579
0.8 73882 15.1695
0.9 156030 32.0362
1.0 819 0.1682
Total 487043

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 223930 78.0056
0.1 15688 5.4649
0.2 10134 3.5302
0.3 9074 3.1609
0.4 7180 2.5011
0.5 5975 2.0814
0.6 4872 1.6972
0.7 4491 1.5644
0.8 3998 1.3927
0.9 1727 0.6016
Total 287069

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 19245 6.7040
0.4 23038 8.0252
0.5 30822 10.7368
0.6 38490 13.4079
0.7 41785 14.5557
0.8 42346 14.7512
0.9 90688 31.5910
1.0 655 0.2282
Total 287069

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 217559 78.4627
0.1 15874 5.7250
0.2 11143 4.0187
0.3 7964 2.8722
0.4 6903 2.4896
0.5 5243 1.8909
0.6 4693 1.6925
0.7 3898 1.4058
0.8 2598 0.9370
0.9 1402 0.5056
Total 277277

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 22961 8.2809
0.4 27154 9.7931
0.5 33062 11.9238
0.6 39327 14.1833
0.7 39590 14.2781
0.8 39770 14.3431
0.9 75123 27.0931
1.0 290 0.1046
Total 277277

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 536945 80.5294
0.1 33785 5.0670
0.2 23771 3.5651
0.3 17738 2.6603
0.4 13772 2.0655
0.5 11846 1.7766
0.6 10070 1.5103
0.7 9647 1.4468
0.8 5822 0.8732
0.9 3373 0.5059
Total 666769

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 59300 8.8936
0.4 73161 10.9725
0.5 86757 13.0116
0.6 95852 14.3756
0.7 92937 13.9384
0.8 91243 13.6843
0.9 166614 24.9883
1.0 905 0.1357
Total 666769

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering